Brain#

This section presents results of brain MRI data. Below are quantitative T1 values computed using the MP2RAGE and the MTsat methods. These values are averaged within the gray matter and white matter masks.

Code imports#

# Python imports 
from IPython.display import clear_output
from pathlib import Path
import numpy as np

import pandas as pd
pd.set_option('display.max_rows', None)
pd.set_option('display.max_columns', None)
pd.set_option('display.width', 1000)
pd.set_option('display.colheader_justify', 'center')
pd.set_option('display.precision', 1)

# Import custom tools
from tools.data import Data
from tools.plot import Plot
from tools.stats import Stats

Download data#

data_type = 'brain'
release_version = 'latest'

dataset = Data(data_type)
dataset.download(release_version)
--2023-02-08 17:27:42--  https://github.com/courtois-neuromod/anat-processing/releases/download/r20220921/neuromod-anat-brain-qmri.zip
Resolving github.com (github.com)... 140.82.114.3
Connecting to github.com (github.com)|140.82.114.3|:443... connected.
HTTP request sent, awaiting response... 
302 Found
Location: https://objects.githubusercontent.com/github-production-release-asset-2e65be/333825187/59a68bb3-4423-49ab-959d-247690acbebc?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20230208%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20230208T172743Z&X-Amz-Expires=300&X-Amz-Signature=36154ac1766ceb782732c4f3f5db7432b4f752c13a0ee04feef37c3de76883fc&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=333825187&response-content-disposition=attachment%3B%20filename%3Dneuromod-anat-brain-qmri.zip&response-content-type=application%2Foctet-stream [following]
--2023-02-08 17:27:43--  https://objects.githubusercontent.com/github-production-release-asset-2e65be/333825187/59a68bb3-4423-49ab-959d-247690acbebc?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20230208%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20230208T172743Z&X-Amz-Expires=300&X-Amz-Signature=36154ac1766ceb782732c4f3f5db7432b4f752c13a0ee04feef37c3de76883fc&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=333825187&response-content-disposition=attachment%3B%20filename%3Dneuromod-anat-brain-qmri.zip&response-content-type=application%2Foctet-stream
Resolving objects.githubusercontent.com (objects.githubusercontent.com)... 185.199.108.133, 185.199.109.133, 185.199.110.133, ...
Connecting to objects.githubusercontent.com (objects.githubusercontent.com)|185.199.108.133|:443... connected.
HTTP request sent, awaiting response... 
200 OK
Length: 1301347 (1.2M) [application/octet-stream]
Saving to: ‘neuromod-anat-brain-qmri.zip’

     0K .......... .......... .......... .......... ..........  3%  426K 3s
    50K .......... .......... .......... .......... ..........  7% 25.0M 1s
   100K .......... .......... .......... .......... .......... 11%  865K 1s
   150K .......... .......... .......... .......... .
......... 15%  845K 1s
   200K .......... .......... .......... .......... .......... 19% 50.6M 1s
   250K .......... .......... .......... .......... .......... 23% 52.2M 1s
   300K .......... .......... .......... .......... .......... 27%  849K 1s
   350K .......... .......... .......... .......... .......... 31%  103M 1s
   400K .......... .......... .......... .......... .......... 35% 6.88M 1s
   450K .......... .......... .......... .......... .......... 39%  963K 1s
   500K .......... .......... .......... .......... .......... 43% 75.7M 0s
   550K .......... .......... .......... .......... .......... 47% 87.8M 0s
   600K .......... .......... .......... .......... .......... 51% 93.3M 0s
   650K .......... .......... .......... .......... .......... 55%  874K 0s
   700K .......... .......... .......... .......... .......... 59% 90.6M 0s
   750K .......... .......... .......... .......... .......... 62%  145M 0s
   800K .......... .......... .......... .......... .......... 66%  138M 0s
   850K .......... .......... .......... .......... .......... 70%  103M 0s
   900K .......... .......... .......... .......... .......... 74% 88.3M 0s
   950K .........
Archive:  neuromod-anat-brain-qmri.zip
  inflating: data/brain/neuromod-anat-brain.nextflow.log  
  inflating: data/brain/results-neuromod-anat-brain-qmri.csv  
  inflating: data/brain/._results-neuromod-anat-brain-qmri.csv  
  inflating: data/brain/dag.dot      
  inflating: data/brain/report.html  
  inflating: data/brain/dag.png      
. .......... .......... .......... .......... 78%  870K 0s
  1000K .......... .......... .......... .......... .......... 82%  271M 0s
  1050K .......... .......... .......... .......... .......... 86% 33.2M 0s
  1100K .......... .......... .......... .......... .......... 90% 86.5M 0s
  1150K .......... .......... .......... .......... .......... 94% 86.1M 0s
  1200K .......... .......... .......... .......... .......... 98%  110M 0s
  1250K .......... ..........                                 100% 79.8M=0.5s

2023-02-08 17:27:44 (2.59 MB/s) - ‘neuromod-anat-brain-qmri.zip’ saved [1301347/1301347]

Load data plot it#

qMRI Metrics#

dataset.load()
fig_gm = Plot(dataset, plot_name = 'brain-1')

fig_gm.title = 'Brain qMRI microstructure measures'
# If you're running this notebook in a Jupyter Notebook (eg, on MyBinder), change 'jupyter-book' to 'notebook'
fig_gm.display('jupyter-book')

Statistics#

White Matter#

stats_wm = Stats(dataset)
stats_wm.build_df('WM')
stats_wm.build_stats_table()
display(stats_wm.stats_table)
T1 (MP2RAGE) T1 (MTsat) MTR MTsat
intrasubject COV mean [%] 0.6 2.3 0.6 1.7
intrasubject COV std [%] 0.2 0.8 0.1 0.5
intersubject mean COV [%] 1.9 3.5 0.4 2.2

Grey Matter#

stats_gm = Stats(dataset)
stats_gm.build_df('GM')
stats_gm.build_stats_table()
display(stats_gm.stats_table)
T1 (MP2RAGE) T1 (MTsat) MTR MTsat
intrasubject COV mean [%] 0.4 3.1 0.8 2.7
intrasubject COV std [%] 0.1 1.6 0.2 1.2
intersubject mean COV [%] 1.0 5.7 1.2 4.5

Diffusion#

data_type = 'brain-diffusion-cc'
release_version = 'latest'

dataset = Data(data_type)
dataset.download(release_version)
--2023-02-08 17:27:45--  https://github.com/courtois-neuromod/anat-processing/releases/download/r20230110/brain-diffusion-cc.zip
Resolving github.com (github.com)... 140.82.112.4
Connecting to github.com (github.com)|140.82.112.4|:443... connected.
HTTP request sent, awaiting response... 
302 Found
Location: https://objects.githubusercontent.com/github-production-release-asset-2e65be/333825187/6e6dd34d-c009-4079-bea8-df5eea106c89?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20230208%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20230208T172745Z&X-Amz-Expires=300&X-Amz-Signature=2c445d1827f7c8485aa65d297971ed3761b36265c557adb2fc48d961a6c6eff9&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=333825187&response-content-disposition=attachment%3B%20filename%3Dbrain-diffusion-cc.zip&response-content-type=application%2Foctet-stream [following]
--2023-02-08 17:27:45--  https://objects.githubusercontent.com/github-production-release-asset-2e65be/333825187/6e6dd34d-c009-4079-bea8-df5eea106c89?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20230208%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20230208T172745Z&X-Amz-Expires=300&X-Amz-Signature=2c445d1827f7c8485aa65d297971ed3761b36265c557adb2fc48d961a6c6eff9&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=333825187&response-content-disposition=attachment%3B%20filename%3Dbrain-diffusion-cc.zip&response-content-type=application%2Foctet-stream
Resolving objects.githubusercontent.com (objects.githubusercontent.com)... 185.199.108.133, 185.199.110.133, 185.199.111.133, ...
Connecting to objects.githubusercontent.com (objects.githubusercontent.com)|185.199.108.133|:443... connected.
HTTP request sent, awaiting response... 
Archive:  brain-diffusion-cc.zip
  inflating: data/brain-diffusion-cc/labels.py  
  inflating: data/brain-diffusion-cc/._labels.py  
  inflating: data/brain-diffusion-cc/.DS_Store  
  inflating: data/brain-diffusion-cc/._.DS_Store  
  inflating: data/brain-diffusion-cc/labels.ipynb  
  inflating: data/brain-diffusion-cc/._labels.ipynb  
  inflating: data/brain-diffusion-cc/corpus_callosum-metrics.csv  
  inflating: data/brain-diffusion-cc/._corpus_callosum-metrics.csv  
200 OK
Length: 15248 (15K) [application/octet-stream]
Saving to: ‘brain-diffusion-cc.zip’

     0K .......... ....                                       100% 35.4M=0s

2023-02-08 17:27:46 (35.4 MB/s) - ‘brain-diffusion-cc.zip’ saved [15248/15248]
dataset.load()

fig_diff = Plot(dataset, plot_name = 'brain-diff-cc')

fig_diff.title = 'Brain qMRI diffusion measures - corpus callosum'

fig_diff.display('jupyter-book')

Statistics#

Genu#

stats_cc1 = Stats(dataset)
stats_cc1.build_df('genu')
stats_cc1.build_stats_table()
display(stats_cc1.stats_table)
FA (DWI) MD (DWI) RD (DWI)
intrasubject COV mean [%] 0.8 1.0 1.3
intrasubject COV std [%] 0.3 0.6 0.6
intersubject mean COV [%] 4.2 6.2 10.3

Body#

stats_cc1 = Stats(dataset)
stats_cc1.build_df('body')
stats_cc1.build_stats_table()
display(stats_cc1.stats_table)
FA (DWI) MD (DWI) RD (DWI)
intrasubject COV mean [%] 0.6 0.7 0.7
intrasubject COV std [%] 0.2 0.2 0.3
intersubject mean COV [%] 3.8 3.0 6.2

Splenium#

stats_cc1 = Stats(dataset)
stats_cc1.build_df('splenium')
stats_cc1.build_stats_table()
display(stats_cc1.stats_table)
FA (DWI) MD (DWI) RD (DWI)
intrasubject COV mean [%] 0.6 0.7 0.8
intrasubject COV std [%] 0.1 0.2 0.3
intersubject mean COV [%] 2.6 3.1 6.3